A Study On Abiogenesis Biology Essay

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Origin Of Life: Abiogenesis

One of the greatest unsolved mysteries of the world is the origin of life, both its circumstances and the first actual life. Nobody knows for certain the exact circumstance of life's origin, so as a result there are plenty of corroborating and conflicting ideas. The mystery surrounding the origin of life may never be solved as there is currently no hard evidence, but what we can do is determine the possibilities for the origin of life. Often times, because of the uncertainty of the subject matter, these possibilities can be conflicting or corroborate with each other.

Did life begin in heat or in cold? What compounds and chemicals made up the atmosphere? Was the first life DNA or RNA? How did the molecules needed for these protocells come together? Where did these molecules come from? What exactly was the first cell? Answering these questions is far to great a task for me so all I want to do is to present several of the current ideas concerning the origin of life, the first cell, and the environment that allowed for the creation of this first protocell. Perhaps in doing so we can learn more of the possibilities of life's origins, the possibilities of life existing elsewhere, and ultimately it may allow us to understand and define what life is.

What is Life?

Before going into what would be required in the original cell, it would be appropriate to note that there is no set definition what life is. As a result, it would be hard to find out what the first of something is, before we can exactly determine what that thing is. Right now, there are several definitions floating around that attempt to define what life is; each has its own merits and drawbacks. Before reaching a conclusion, lets examine a few of the potential possibilities for a definition of life.

Campbell defines life partly as requiring two things: accurate replication and metabolism.1 However, this definition poses a problem, as each trait requires the other. For example, the genetic information for in DNA, which has the information necessary for replication, alone, does not have the necessary "enzymatic machinery" or the nucleotides necessary for replication. Essentially, it is a veritable chicken or the egg situation where either answer has its own problem. An interesting possible solution though is to change the question from "this or that" to a situation where both the "chicken", or the metabolism, and the "egg", or the accurate replication, came to being at the same time.

Other definitions introduce key ideas that could be part of definition of life. One definition put forward by physicist Erwin Schrödinger includes that a key feature of life be that it works against nature's tendency towards disorder. 2 One should note in this definition doesn't say that life defies the laws of thermodynamics, rather it attempts to say that life is growing in a universe where the norm is two disorganize. Gerald Joyce writes that life may be defined "a self-sustaining chemical system capable of Darwinian Evolution."3 This definition includes a necessary and interesting point about the need for an evolutionary component in life. A third definition proposed by Carl Sagan in the Encyclopedia Britannica uses a thermodynamic, rather than genetic, approach to life defining it as a localized region which increases in order through cycles driven by an energy. 4 This definition would be a broadening of what we currently deem to be life and allows for greater freedom and simplicity in defining it life. By leaving the realm of the genetics, this definition provides a new perspective on what we've been thinking life is.

Robert Shapiro, in his article A Simpler Origin published in February 2007, defined life under five criteria, which serve as a relatively good synthesis of all of the above. The five ideas are as follows: "(1) A boundary is needed to separate life from non-life. (2) An energy source is needed to drive the organization process. (3) A coupling mechanism must link the release of energy to the organization process that produces and sustains life. (4) A chemical network must be formed, to permit adaptation and evolution. (5) The network must grow and reproduce." His ideas specify the idea of a boundary for life, specifically define the concept of organization or order within life, and incorporate other ideas such as evolution as key component of life, rather than a byproduct of life. This sort of definition, one that is inclusive to other ideas, explicit, yet broad in scope, sets an example in what we should strive for in defining life. 5

One should note that single definition of life that is accepted by the scientific community and that no working definition is either broad or specific enough to account for life forms that we have yet to see. These forms that we have yet to encounter could be alien or they could be instead very early life forms including the very first cell and it's constituent parts. So all I can say in response to the question "What is life?" is to keep an open mind.

Protocells

Protocells, or the first primitive cells which would have to extremely simple yet complex enough to fall under a definition of life, probably looked very different from the cells which we now are used to seeing. They probably consisted of a simple lipid membrane with RNA acting as the genetic material. Although there has been no decisive evidence, as no one has created a protocell capable of self-replicating, there are many reasons to think RNA is the genetic material. Another mystery that is baffling scientists is exactly how the RNA formed, or more specifically how nucleotides or other molecules used to create RNA formed in the environment of early earth. Basically there were three things that need to be considered in the protocell, discovering substances required for the formation of RNA, the actual formation of the RNA, and then a membrane to separate it from the outside environment.

As for the substances required for the formation of RNA molecules, they would have to exist on an early earth, which had greatly different atmosphere and consisted of several different molecules. However, the environment in which these molecules formed will be discuss later in this paper. For now, I will focus on the components of RNA. An RNA nucleotide consists of a nucleotide base, a sugar and phosphate backbone. The nucleotide bases are capable of spontaneously forming provided there are the starting molecules of cyanide, acetylene, and water. The sugar, ribose, which is needed for RNA can also form spontaneously, but would be unstable in the earth's early environment. Another problem with the formation of the sugar, ribose, is that sugars many other sugars could form by this method, and it would not lead to an surplus of ribose but merely several other sugars. Phosphorus, necessary for the final component of RNA, phosphate, existed in pre-biotic earth's crust in large amounts but is not soluble in water, which is most likely where life started to occur. However, phosphorus forms that are soluble in water could have came from a number of other places. One possibility is volcanic vents changing phosphorus into soluble forms by application of extreme heat. This method, though, only produces limited amounts of the soluble phosphorus, and for the creation of a protocell an abundance of nucleotide bases would be necessary. Another more feasible possibility is phosphorus coming from an extra-terrestrial source. Meteors that held a variety of substances continually hit Prebiotic earth; one common mineral found in meteorites is schreibersite, which has a readily soluble version of phosphorus.

Looking at all of the above evidence, it becomes clear that the spontaneous formation of the main components of RNA is exceedingly unlikely. Furthermore another problem arises when attempting to combine these components; only adding the phosphate, nucleotide base, and sugar together to water does not make them combine. For the components to combine energy rich compounds must supply the energy to the components, however the results are at best inefficient.

Gathering from these facts we can conclude that RNA, if it was the first genetic material, did not form through this manner. Another more promising manner that RNA was formed uses the same initial molecules, but instead combines them in different reactions with the end result of RNA. Using the initial molecules of various versions of cyanide, acetylene, and formaldehyde John Sutherland and scientists at the University of Manchester discovered that one could combine these initial substances with phosphate rather than making the sugar and nucleotide base combining them, and then adding the phosphate. (Details can be seen in diagram 1). Once again, this seems a more likely method as the sugar and base are unstable and don't combine very well. Furthermore, this process seems more likely because even though it may produce nucleotides with the wrong spatial organization, an inevitable occurrence, UV rays destroy these same wrong nucleotides. However this method is not without its own problems. For instance, one of the key intermediates aminooxazole-2 is highly volatile which may have prevented it from accumulating in large amounts, which would be necessary for the abiotic synthesis of life.

Next, comes the issue of how the nucleotide monomers came together to form polymers. We have already established that under normal conditions the monomers do not bond with each other. With this knowledge, we can deduce that there are external forces that either catalyze the reaction or directly add energy to allow for the reaction. Scientists have discovered that certain layers of clay catalyze the formation of polymers. The way these clay layers work is by bringing the monomers closer together and making them more likely to react with one another. This particular area of abiogenesis, the abiotic synthesis of polymers, is still blurry and is still subject to more research.

And now the last component of required for the protocell, the membrane, which would separate the cell from non-life. The membrane would have to spontaneously form without the aid of enzymes or proteins. The membrane would also have to be much simpler, and the mechanisms for repair and maintenance of the membrane would also have to be much simpler because of the lack of proteins with specific functions.

An idea proposed by Jack W. Szostak proposes that membrane must have been self-replicating as there were no mechanisms for cell division and growth. 6 Because the genetic material's, RNA, initial primary function would have been catalyzing its own synthesis and not dealing with the membrane, the membrane would need to be able to spontaneously grow and divide at similar times relative to the RNA. Obviously, the two mechanisms must not interfere with each other.

The proposed membrane for protocells is a liposome or a membrane composed of lipids. Lipids, which existed in Prebiotic earth, can spontaneously form into a membrane when placed in water. Liposomes can grow either through addition of single lipids or through the combining of vesicles; either method is simple and doesn't require additional "help". Now, here's where the problem of division occurs. There is no simple cellular mechanism that would allow the membrane and RNA to divide at similar time. In the absence of these mechanisms we turn to the environment. The current theories suggest that heat was the agent that simultaneously divided the membrane and perhaps split the double RNA strands (where one strand was used as template to make another).

One issue that arises is the how this membrane would be selectively permeable and how it would incorporate nucleotides. Very simply, the primitive lipid membrane would allow nucleotides to pass through because it wouldn't be as selectively permeable as current membranes of cells. In addition we have the very possible situation where the membranes formed around nucleotides.

The RNA World

Now we have gone over the various substances required for monomers, where the substances came from, the abiotic synthesis of monomers, and the abiotic synthesis of polymers, synthesis and constitution of the membrane. However it seems necessary to discuss why in the first place RNA was the genetic material rather than DNA.

RNA seems to be the genetic material first and foremost because it can do many functions that DNA can't. One example would be RNA's ability to act as enzyme. RNA has this ability because, as a single strand, it has the ability to fold into different forms based on the nucleotide sequences. The different nucleotide sequences create different shapes in the RNA because different orders change the number and arrangement of bonds between the nucleotides. A very interesting possibility is that a few of these forms may catalyze the reaction for the synthesis. Furthermore, this ability to replicate is one of the key properties of life and so it seems that RNA's unique ability for self-replication perfectly suits early life. RNA also has the function of being used as a template to form proteins, which we know do most of the work within a cell.

DNA, on the other hand, really only functions as a template for RNA, which in turn forms proteins. If you think about it RNA can serve both as the metabolism and allows for replication. It serves as metabolism, seen in the ability to code for proteins, and replication, which can be seen in ribozyme's possibility for replication. DNA, however, requires external help to do both functions; DNA needs enzymes to replicate, and enzymes and RNA for metabolism. RNA is looking to be a very good candidate for the genetic material of the first cell.

Another key component of life as I have already mentioned is that it must be "capable of undergoing Darwinian evolution". RNA molecules have, in their own way, the ability to go through natural selection. 7 The way that RNA molecules could be selected for lies in the variability of the forms of RNA. RNA molecules with forms that catalyzed reactions faster and more stable reactions and with more stable forms could become increasingly common to the less fast and stable forms of RNA. The stability of these forms could be due to both inherent genetics or due to environment. In other words some molecules would more suited to their environment then others. Thus it would create a differential in "reproductive" success and a change in abundance of a particular variety of RNA. Because RNA doesn't replicate perfectly it would allow for even more genetic variability and would allow for future evolution of the RNA genome.

Judging from these ideas, it seems clear that RNA is most likely the genetic material in the first cell. Reiterating the points above, RNA can act as enzymes and catalyze reactions (including it's own synthesis), code for proteins, and allow for Darwinian evolution.

Conditions Necessary for Life

Currently, there is large debate over what exactly pre-biotic earth was composed of and under what conditions did life arise. Some of the larger issues of controversy have been over temperature and have dealt with the molecules making up early earth.

Most theories of the beginning of life either have life begin in extreme heat or in extreme cold. To start, I would like to explain the merits of heat. Having the life begin in heat would allow for the previously stated ability to divide RNA strands, and to divide the primitive lipid membrane. Another merit of heat is that it allows for an increase in reaction rate. Reaction rate is a key component in the origin of life. This is due to the fact that many reactions without the aid of enzymes, which were largely absent in this early earth, occur either extremely slowly or don't occur at all. In all cases there is need to discover the circumstances that would increase reaction rate. The main theory concerning heat, proposed by A. I. Oparin, suggests that the origin of life occurred a "primordial soup" that is oceans of organic molecules.

The famous Miller-Urey experiment showed that under the conditions thought to be in prebiotic earth that organic molecules could be formed from simple molecules. The conditions that Miller and Urey used were as follows: the atmosphere consisted of methane, hydrogen, and ammonia they used warm water to represent the primordial soup, thought the atmosphere was a reducing atmosphere, and used a spark to simulate lightning. In a reducing environment, with the addition of energy (in the form of lightning), organic compounds could have formed from simple molecules.

However, now most of their conditions that were used have now been shown to be incorrect; the amount of methane and hydrogen did not exist in abundance, rather earth had an neither a reducing or oxidizing atmosphere, and the gases that were abundant were carbon dioxide and nitrogen.9 When the experiment was redone with the changes in the environment, it resulted in much fewer amino acids.10 But now Jeffrey Bada's has repeated the experiment, who's results were published in Scientific American in March of 2007, noting that the reaction was creating nitrites, which destroy amino acids. He noted, though, that prebiotic earth contained minerals that would have neutralized the nitrites making them harmless to the amino acids. And so when he repeated the experiment with the nitrites removed, the result was the formation of many amino acids, once again bringing merit to the warm primordial soup theory.

This brings me to the theory that life began in the cold rather than in heat. Normally one would expect that reaction rate lowers as temperature lowers, and for the most part one is correct. However, just as some reactions rates lower so do other reaction rates increase. One of the few kinds of reactions that speeds up as temperature lowers is the joining of small molecules into larger molecules.8 To put it in terms of abiogenesis, cold temperatures would actually allow for the joining monomers into polymers, which would greatly assist in the formation of RNA. The process by which this works is called eutectic freezing. It works like this: when an ice crystal forms, it excludes all impurities and only adds water. Other substances are excluded in the crystal and form microscopic pockets of liquid where the molecules are more likely to combine with each other. In other words eutectic freezing although it lowers the reaction rate purely based on temperature, overall can speed up reaction rate based on the concentration of substances.

Stanley Miller had a twenty-five year long experiment starting in 1972 where he filled a vial with a mixture of ammonia and cyanide, chemicals that are necessary components for life and were thought to have existed on Prebiotic Earth. He placed a vial in a freezer and kept it at negative 108 degrees for the entire time. When testing the vial in 1997, he discovered that the molecules had combined to form nucleotide bases. This experiment largely shifted the paradigm of most of the theories on the beginnings of life, introducing the unheard of possibility that life occurred in the cold rather than in warmth.

In The End

Overall, when considering the subject of abiogenesis and the origin of life we should strive to keep our minds open because even after reviewing these numerous ideas, I've come to the realization that I've only barely scratched the surface of this huge topic. I've learned that there is no perfect answer as for life's origin and it's likely that we may never know what happened. However, searching for the possibilities will allow us to better understand life and ultimately will lead us to a clearer perspective on life.

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